相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Current RNA-seq methodology reporting limits reproducibility
Joel Simoneau et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Toward a domain-specific language for scientific workflow-based applications on multicloud system
Gennaro Cordasco et al.
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE (2021)
PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection
Martin Hoelzer et al.
BIOINFORMATICS (2021)
Streamlining data-intensive biology with workflow systems
Taylor Reiter et al.
GIGASCIENCE (2021)
Reproducibility in systems biology modelling
Krishna Tiwari et al.
MOLECULAR SYSTEMS BIOLOGY (2021)
Using prototyping to choose a bioinformatics workflow management system
Michael Jackson et al.
PLOS COMPUTATIONAL BIOLOGY (2021)
Why reinventing the wheels? An empirical study on library reuse and re-implementation
Bowen Xu et al.
EMPIRICAL SOFTWARE ENGINEERING (2020)
Butler enables rapid cloud-based analysis of thousands of human genomes
Sergei Yakneen et al.
NATURE BIOTECHNOLOGY (2020)
The nf-core framework for community-curated bioinformatics pipelines
Philip A. Ewels et al.
NATURE BIOTECHNOLOGY (2020)
Bench pressing with genomics benchmarkers
Vivien Marx
NATURE METHODS (2020)
Scalable Data Analysis in Proteomics and Metabolomics Using BioContainers and Workflows Engines
Yasset Perez-Riverol et al.
PROTEOMICS (2020)
Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Michael I. Love et al.
PLOS COMPUTATIONAL BIOLOGY (2020)
Better together: Elements of successful scientific software development in a distributed collaborative community
Julia Koehler Leman et al.
PLoS Computational Biology (2020)
Seven quick tips for analysis scripts in neuroimaging
Marijn van Vliet
PLoS Computational Biology (2020)
Variability in the analysis of a single neuroimaging dataset by many teams
Rotem Botvinik-Nezer et al.
NATURE (2020)
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
Vahid Jalili et al.
NUCLEIC ACIDS RESEARCH (2020)
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
Silas Kieser et al.
BMC BIOINFORMATICS (2020)
Scalability and cost-effectiveness analysis of whole genome-wide association studies on Google Cloud Platform and Amazon Web Services
Ines Krissaane et al.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION (2020)
Ten recommendations for supporting open pathogen genomic analysis in public health
Allison Black et al.
NATURE MEDICINE (2020)
FAIR Computational Workflows
Carole Goble et al.
DATA INTELLIGENCE (2020)
Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures
Joel Simoneau et al.
NAR GENOMICS AND BIOINFORMATICS (2020)
Practical estimation of cloud storage costs for clinical genomic data
Niklas Krumm et al.
PRACTICAL LABORATORY MEDICINE (2020)
An empirical comparison of dependency network evolution in seven software packaging ecosystems
Alexandre Decan et al.
EMPIRICAL SOFTWARE ENGINEERING (2019)
Container-based bioinformatics with Pachyderm
Jon Ander Novella et al.
BIOINFORMATICS (2019)
Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data
Robert L. Grossman
TRENDS IN GENETICS (2019)
snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
Vivek Bhardwaj et al.
BIOINFORMATICS (2019)
In silico analysis of RNA-seq requires a more complete description of methodology
Joel Simoneau et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)
SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
Samuel Lampa et al.
GIGASCIENCE (2019)
TIPS FOR OPEN-SOURCE SOFTWARE SUPPORT
Anna Nowogrodzki
NATURE (2019)
Challenges and recommendations to improve the installability and archival stability of omics computational tools
Serghei Mangul et al.
PLOS BIOLOGY (2019)
CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language
Michael Kotliar et al.
GIGASCIENCE (2019)
GenPipes: an open-source framework for distributed and scalable genomic analyses
Mathieu Bourgey et al.
GIGASCIENCE (2019)
THAT'S THE WAY WE FLOW
Jeffrey M. Perkel
NATURE (2019)
Essential guidelines for computational method benchmarking
Lukas M. Weber et al.
GENOME BIOLOGY (2019)
Challenges in funding and developing genomic software: roots and remedies
Adam Siepel
GENOME BIOLOGY (2019)
Programming models and systems for Big Data analysis
Loris Belcastro et al.
INTERNATIONAL JOURNAL OF PARALLEL EMERGENT AND DISTRIBUTED SYSTEMS (2019)
VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
MacIntosh Cornwell et al.
BMC BIOINFORMATICS (2018)
LncPipe: A Nextflow-based pipeline for identification and analysis of long non-coding RNAs from RNA-Seq data
Qi Zhao et al.
JOURNAL OF GENETICS AND GENOMICS (2018)
Bioconda: sustainable and comprehensive software distribution for the life sciences
Bjoern Gruening et al.
NATURE METHODS (2018)
Cloud computing for genomic data analysis and collaboration
Ben Langmead et al.
NATURE REVIEWS GENETICS (2018)
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Enis Afgan et al.
NUCLEIC ACIDS RESEARCH (2018)
An empirical analysis of journal policy effectiveness for computational reproducibility
Victoria Stodden et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Practical Computational Reproducibility in the Life Sciences
Bjoern Gruening et al.
CELL SYSTEMS (2018)
Community-Driven Data Analysis Training for Biology
Berenice Batut et al.
CELL SYSTEMS (2018)
Top considerations for creating bioinformatics software documentation
Mehran Karimzadeh et al.
BRIEFINGS IN BIOINFORMATICS (2018)
GitHub Statistics as a Measure of the Impact of Open-Source Bioinformatics Software
Mikhail G. Dozmorov
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2018)
Raw data queries during data-intensive parallel workflow execution
Vitor Silva et al.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE (2017)
KNIME for reproducible cross-domain analysis of life science data
Alexander Fillbrunn et al.
JOURNAL OF BIOTECHNOLOGY (2017)
Reproducibility of computational workflows is automated using continuous analysis
Brett K. Beaulieu-Jones et al.
NATURE BIOTECHNOLOGY (2017)
Nextflow enables reproducible computational workflows
Paolo Di Tommaso et al.
NATURE BIOTECHNOLOGY (2017)
Toil enables reproducible, open source, big biomedical data analyses
John Vivian et al.
NATURE BIOTECHNOLOGY (2017)
Ten Simple Rules for Developing Usable Software in Computational Biology
Markus List et al.
PLOS COMPUTATIONAL BIOLOGY (2017)
Scalability and Validation of Big Data Bioinformatics Software
Andrian Yang et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2017)
Singularity: Scientific containers for mobility of compute
Gregory M. Kurtzer et al.
PLOS ONE (2017)
The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research
Jessica W. Lau et al.
CANCER RESEARCH (2017)
Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis
Steffen Moeller et al.
DATA SCIENCE AND ENGINEERING (2017)
Investigating reproducibility and tracking provenance - A genomic workflow case study
Sehrish Kanwal et al.
BMC BIOINFORMATICS (2017)
BioContainers: an open-source and community-driven framework for software standardization
Felipe da Veiga Leprevost et al.
BIOINFORMATICS (2017)
Community curation in open dataset repositories: insights from Zenodo
Miguel-Angel Sicilia et al.
13TH INTERNATIONAL CONFERENCE ON CURRENT RESEARCH INFORMATION SYSTEMS, CRIS2016, COMMUNICATING AND MEASURING RESEARCH RESPONSIBLY: PROFILING, METRICS, IMPACT, INTEROPERABILITY (2017)
Coming of age: ten years of next-generation sequencing technologies
Sara Goodwin et al.
NATURE REVIEWS GENETICS (2016)
deepTools2: a next generation web server for deep-sequencing data analysis
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2016)
Big Data: Astronomical or Genomical?
Zachary D. Stephens et al.
PLOS BIOLOGY (2015)
A modular package manager architecture
Pietro Abate et al.
INFORMATION AND SOFTWARE TECHNOLOGY (2013)
Bpipe: a tool for running and managing bioinformatics pipelines
Simon P. Sadedin et al.
BIOINFORMATICS (2012)
Snakemake-a scalable bioinformatics workflow engine
Johannes Koester et al.
BIOINFORMATICS (2012)
The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements
Ed H. B. M. Gronenschild et al.
PLOS ONE (2012)
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
Aaron McKenna et al.
GENOME RESEARCH (2010)
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Jeremy Goecks et al.
GENOME BIOLOGY (2010)
分享论文
